Package: methylInheritance 1.37.0

Astrid Deschênes

methylInheritance: Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.

Authors:Astrid Deschênes [cre, aut], Pascal Belleau [aut], Arnaud Droit [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
methylInheritance/json (API)

# Install 'methylInheritance' in R:

install.packages('methylInheritance', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adeschen/methylinheritance/issues

Datasets:

demoForTransgenerationalAnalysis - The methylation information from samples over three generations. Information for each generation is stored in a 'methylRawList' format (for demo purpose).
methylInheritanceResults - All observed and permutation results formatted in a 'methylInheritanceResults' class (for demo purpose).
samplesForTransgenerationalAnalysis - All samples information, formated by 'methylKit', in a 'methylRawList' format (for demo purpose).

On BioConductor:methylInheritance-1.37.0(bioc 3.24)methylInheritance-1.36.0(bioc 3.23)

biologicalquestion epigenetics dnamethylation differentialmethylation methylseq software immunooncology statisticalmethod wholegenome sequencing analysis bioconductor bioinformatics cpg differentially-methylated-elements inheritance monte-carlo-sampling permutation

4.88 score 1 scripts 9 exports 97 dependencies

Last updated from:a2ea86b980. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	271
linux-devel-x86_64	OK	528
source / vignettes	OK	343
linux-release-x86_64	OK	552
macos-release-arm64	OK	388
macos-oldrel-arm64	OK	345
windows-devel	OK	476
windows-release	OK	338
windows-oldrel	OK	472
wasm-release	OK	185

Exports:calculateSignificantLevel extractInfo loadAllRDSResults loadConvergenceData mergePermutationAndObservation plotConvergenceGraph plotGraph runObservation runPermutation

Dependencies:abind askpass bbmle bdsmatrix BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops cigarillo cli coda codetools cpp11 crayon curl data.table DelayedArray emdbook farver fastseg formatR futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gridExtra gtable gtools httr IRanges isoband jsonlite KernSmooth labeling lambda.r lattice lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats mclust methylKit mgcv mime mvtnorm nlme numDeriv openssl plyr qvalue R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl rebus rebus.base rebus.datetimes rebus.numbers rebus.unicode reshape2 restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment sys vctrs viridisLite withr XML XVector yaml

Inferring inheritance of differentially methylated changes across multiple generations

Rendered frommethylInheritance.Rmdusingknitr::rmarkdown

Last update: 2018-11-30
Started: 2017-04-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate significant level for hypo and hyper conserved elements	calculateSignificantLevel
The methylation information from samples over three generations. Information for each generation is stored in a 'methylRawList' format (for demo purpose).	demoForTransgenerationalAnalysis
Extract the information specific to a subsection of the permutation analysis	extractInfo
Load all RDS files created by the permutation and observation analysis	loadAllRDSResults
Load convergence information from RDS files	loadConvergenceData
Merge the permutation results with the observation results.	mergePermutationAndObservation
All observed and permutation results formatted in a 'methylInheritanceResults' class (for demo purpose).	methylInheritanceResults
Generate a graph showing the convergence for a permutation analysis	plotConvergenceGraph
Generate a graph for a permutation analysis	plotGraph
Print a 'methylInheritanceAllResults' object	print.methylInheritanceAllResults
Run a differential methylation analysis on multi-generational dataset	runObservation
Run all permutations on the specified multi-generational dataset	runPermutation
All samples information, formated by 'methylKit', in a 'methylRawList' format (for demo purpose).	samplesForTransgenerationalAnalysis